Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2802 (918269a29b*) started at 2026-07-29T14:25:49.610 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.79s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Installed CommonWorldInvalidations ───────── v1.1.1 Installed CommonSolve ────────────────────── v0.2.12 Installed DataStructures ─────────────────── v0.19.6 Installed GLM ────────────────────────────── v1.9.5 Installed Glob ───────────────────────────── v1.5.0 Installed MacroTools ─────────────────────── v0.5.16 Installed CompositionsBase ───────────────── v0.1.2 Installed CodecZstd ──────────────────────── v0.8.7 Installed VCFTools ───────────────────────── v0.2.10 Installed FilePathsBase ──────────────────── v0.9.24 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed ManualMemory ───────────────────── v0.1.8 Installed Adapt ──────────────────────────── v4.7.0 Installed FillArrays ─────────────────────── v1.17.0 Installed StatsModels ────────────────────── v0.7.10 Installed HypergeometricFunctions ────────── v0.3.29 Installed VectorizationBase ──────────────── v0.21.74 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed ConstructionBase ───────────────── v1.6.0 Installed InlineStrings ──────────────────── v1.4.5 Installed SLEEFPirates ───────────────────── v0.6.46 Installed StatsBase ──────────────────────── v0.34.12 Installed DelimitedFiles ─────────────────── v1.9.1 Installed AliasTables ────────────────────── v1.1.3 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed CodecZlib ──────────────────────── v0.7.8 Installed SIMDTypes ──────────────────────── v0.1.0 Installed ArrayInterface ─────────────────── v7.28.1 Installed CSV ────────────────────────────── v0.10.16 Installed TranscodingStreams ─────────────── v0.9.13 Installed OrderedCollections ─────────────── v2.0.1 Installed ShiftedArrays ──────────────────── v2.0.0 Installed LoopVectorization ──────────────── v0.12.174 Installed HypothesisTests ────────────────── v0.11.8 Installed Compat ─────────────────────────── v4.18.1 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed SIMD ───────────────────────────── v3.7.2 Installed DataAPI ────────────────────────── v1.16.0 Installed Combinatorics ──────────────────── v1.1.0 Installed HostCPUFeatures ────────────────── v0.1.18 Installed Statistics ─────────────────────── v1.11.1 Installed InvertedIndices ────────────────── v1.3.1 Installed CpuId ──────────────────────────── v0.3.1 Installed StatsAPI ───────────────────────── v1.8.0 Installed ProgressMeter ──────────────────── v1.11.0 Installed dlfcn_win32_jll ────────────────── v1.4.2+0 (no artifacts on this platform) Installed OffsetArrays ───────────────────── v1.17.0 Installed DataValueInterfaces ────────────── v1.0.0 Installed PrecompileTools ────────────────── v1.3.4 Installed SentinelArrays ─────────────────── v1.4.10 Installed StringManipulation ─────────────── v0.4.6 Installed SciMLPublic ────────────────────── v1.2.4 Installed IrrationalConstants ────────────── v0.2.6 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed QuadGK ─────────────────────────── v2.11.3 Installed LayoutPointers ─────────────────── v0.1.17 Installed StaticArrayInterface ───────────── v1.10.0 Installed CPUSummary ─────────────────────── v0.2.7 Installed Distances ──────────────────────── v0.10.12 Installed Requires ───────────────────────── v1.3.1 Installed LogExpFunctions ────────────────── v1.0.1 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed Roots ──────────────────────────── v3.0.6 Installed Parsers ────────────────────────── v2.8.6 Installed Gamma ──────────────────────────── v1.1.0 Installed BufferedStreams ────────────────── v1.2.2 Installed Distributions ──────────────────── v0.25.130 Installed PrettyTables ───────────────────── v3.4.2 Installed BioGenerics ────────────────────── v0.1.5 Installed StatsFuns ──────────────────────── v2.2.0 Installed Tables ─────────────────────────── v1.13.0 Installed Rmath ──────────────────────────── v0.9.0 Installed SpecialFunctions ───────────────── v2.8.0 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed IfElse ─────────────────────────── v0.1.1 Installed PtrArrays ──────────────────────── v1.4.0 Installed Reexport ───────────────────────── v1.2.2 Installed Static ─────────────────────────── v1.4.4 Installed InverseFunctions ───────────────── v0.1.17 Installed Missings ───────────────────────── v1.2.0 Installed DataFrames ─────────────────────── v1.8.2 Installed Preferences ────────────────────── v1.5.2 Installed BGEN ───────────────────────────── v0.1.17 Installed WeakRefStrings ─────────────────── v1.4.3 Installed DBInterface ────────────────────── v2.6.1 Installed PooledArrays ───────────────────── v1.4.3 Installed JLLWrappers ────────────────────── v1.8.0 Installed TableTraits ────────────────────── v1.0.1 Installed SortingAlgorithms ──────────────── v1.2.3 Installed SnpArrays ──────────────────────── v0.3.23 Installed LaTeXStrings ───────────────────── v1.4.0 Installed Automa ─────────────────────────── v1.2.0 Installed PDMats ─────────────────────────── v0.11.40 Installed Crayons ────────────────────────── v4.2.0 Installed SQLite ─────────────────────────── v1.8.1 Installed SQLite_jll ─────────────────────── v3.53.2+0 Installed VariantCallFormat ──────────────── v0.5.9 Installed ThreadingUtilities ─────────────── v0.5.6 Installed XZ_jll ─────────────────────────── v5.8.3+0 Installed BGZFStreams ────────────────────── v0.3.2 Installed CodecXz ────────────────────────── v0.7.4 Installed Accessors ──────────────────────── v0.1.45 Installed PolyesterWeave ─────────────────── v0.2.2 Installed UnPack ─────────────────────────── v1.0.2 Installed WorkerUtilities ────────────────── v1.6.1 Installed DocStringExtensions ────────────── v0.9.5 Installed MendelIHT ──────────────────────── v1.4.11 Installing 6 artifacts Installed artifact SQLite 1.2 MiB Installed artifact Rmath 111.5 KiB Installed artifact OpenSpecFun 105.4 KiB Installed artifact Bzip2 152.8 KiB Installed artifact XZ 1018.2 KiB Installed artifact testfiles 4.4 MiB Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.28.1 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.12 [f70d9fcc] + CommonWorldInvalidations v1.1.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.130 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.17.0 [38e38edf] + GLM v1.9.5 [a0844989] + Gamma v1.1.0 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.29 [09f84164] + HypothesisTests v0.11.8 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v1.0.1 [bdcacae8] + LoopVectorization v0.12.174 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v2.0.1 [90014a1f] + PDMats v0.11.40 [69de0a69] + Parsers v2.8.6 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.4.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.6 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [0aa819cd] + SQLite v1.8.1 [431bcebd] + SciMLPublic v1.2.4 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.8.0 [aedffcd0] + Static v1.4.4 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.4.6 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.13.0 [8290d209] + ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.74 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [76ed43ae] + SQLite_jll v3.53.2+0 [ffd25f8a] + XZ_jll v5.8.3+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] + LibCURL_jll v8.21.0+0 [e37daf67] + LibGit2_jll v1.9.6+0 [29816b5a] + LibSSH2_jll v1.11.103+0 [14a3606d] + MozillaCACerts_jll v2026.7.16 [4536629a] + OpenBLAS_jll v0.3.34+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 14.51s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.3 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.6 s ✓ MacroTools 1.5 s ✓ InlineStrings 0.5 s ✓ Reexport 0.7 s ✓ ConstructionBase 2.0 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.5 s ✓ StatsAPI 2.2 s ✓ Combinatorics 0.4 s ✓ CommonSolve 0.6 s ✓ LaTeXStrings 0.6 s ✓ Glob 0.8 s ✓ Statistics 0.4 s ✓ IfElse 0.5 s ✓ PtrArrays 0.6 s ✓ ManualMemory 0.6 s ✓ Adapt 0.5 s ✓ DataAPI 0.5 s ✓ SciMLPublic 0.6 s ✓ CommonWorldInvalidations 0.5 s ✓ InvertedIndices 0.7 s ✓ InverseFunctions 0.5 s ✓ CompositionsBase 0.6 s ✓ ShiftedArrays 0.7 s ✓ WorkerUtilities 2.3 s ✓ FillArrays 0.5 s ✓ UnPack 0.5 s ✓ DBInterface 1.0 s ✓ OrderedCollections 0.7 s ✓ DocStringExtensions 0.9 s ✓ Gamma 1.1 s ✓ OffsetArrays 0.6 s ✓ BufferedStreams 0.4 s ✓ SIMDTypes 0.5 s ✓ IteratorInterfaceExtensions 1.7 s ✓ Crayons 0.7 s ✓ Requires 1.9 s ✓ ProgressMeter 0.7 s ✓ DelimitedFiles 1.8 s ✓ SentinelArrays 1.7 s ✓ StructUtils 1.4 s ✓ CpuId 2.0 s ✓ PDMats 0.7 s ✓ Compat 1.3 s ✓ Preferences 1.8 s ✓ TranscodingStreams 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1.5 s ✓ Statistics → SparseArraysExt 1.0 s ✓ Distances 0.6 s ✓ AliasTables 1.3 s ✓ ThreadingUtilities 0.8 s ✓ ArrayInterface 1.4 s ✓ Adapt → AdaptSparseArraysExt 0.6 s ✓ Missings 0.7 s ✓ PooledArrays 1.0 s ✓ InverseFunctions → InverseFunctionsDatesExt 1.4 s ✓ InverseFunctions → InverseFunctionsTestExt 0.5 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.8 s ✓ FillArrays → FillArraysSparseArraysExt 0.9 s ✓ FillArrays → FillArraysStatisticsExt 3.3 s ✓ DataStructures 1.0 s ✓ LogExpFunctions 1.7 s ✓ HypergeometricFunctions 0.6 s ✓ OffsetArrays → OffsetArraysAdaptExt 0.6 s ✓ TableTraits 2.0 s ✓ FillArrays → FillArraysPDMatsExt 0.5 s ✓ Compat → CompatLinearAlgebraExt 1.5 s ✓ PrecompileTools 1.2 s ✓ JLLWrappers 1.5 s ✓ BioGenerics 1.7 s ✓ CodecZstd 1.1 s ✓ CodecZlib 1.4 s ✓ Distances → DistancesSparseArraysExt 0.8 s ✓ ArrayInterface → ArrayInterfaceFillArraysExt 1.3 s ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 3.8 s ✓ Accessors 0.7 s ✓ SortingAlgorithms 2.0 s ✓ QuadGK 0.6 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1.6 s ✓ Tables 2.4 s ✓ FilePathsBase 6.6 s ✓ StringManipulation 12.9 s ✓ SIMD 19.0 s ✓ Automa 10.1 s ✓ Parsers 2.3 s ✓ Static 1.6 s ✓ Bzip2_jll 1.2 s ✓ XZ_jll 1.0 s ✓ Rmath_jll 1.1 s ✓ OpenSpecFun_jll 1.1 s ✓ dlfcn_win32_jll 1.4 s ✓ BGZFStreams 1.6 s ✓ Accessors → TestExt 2.8 s ✓ Accessors → LinearAlgebraExt 4.8 s ✓ StatsBase 0.8 s ✓ StructUtils → StructUtilsTablesExt 2.6 s ✓ FilePathsBase → FilePathsBaseTestExt 0.8 s ✓ FilePathsBase → FilePathsBaseMmapExt 44.7 s ✓ PrettyTables 7.0 s ✓ JSON 0.8 s ✓ InlineStrings → ParsersExt 0.8 s ✓ BitTwiddlingConvenienceFunctions 2.7 s ✓ CPUSummary 3.0 s ✓ StaticArrayInterface 1.9 s ✓ CodecBzip2 1.6 s ✓ CodecXz 1.5 s ✓ Rmath 5.4 s ✓ SpecialFunctions 1.2 s ✓ SQLite_jll [ Info: Compiling VCF parser... 16.5 s ✓ VariantCallFormat 5.6 s ✓ Roots 1.7 s ✓ PDMats → StatsBaseExt 88.2 s ✓ DataFrames 10.5 s ✓ BenchmarkTools 2.2 s ✓ WeakRefStrings 2.5 s ✓ HostCPUFeatures 1.9 s ✓ PolyesterWeave 1.0 s ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1.1 s ✓ CloseOpenIntervals 1.1 s ✓ LayoutPointers 2.0 s ✓ StatsFuns 24.3 s ✓ CSV 4.4 s ✓ SQLite 15.9 s ✓ VectorizationBase 1.2 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 5.3 s ✓ StatsModels 3.6 s ✓ BGEN 2.6 s ✓ SLEEFPirates 10.4 s ✓ Distributions 42.0 s ✓ LoopVectorization 6.2 s ✓ GLM 4.5 s ✓ Distributions → DistributionsTestExt 5.0 s ✓ HypothesisTests 3.3 s ✓ LoopVectorization → SpecialFunctionsExt 6.2 s ✓ VCFTools julia: /source/src/staticdata.c:216: jl_object_in_image: Assertion `eyt_tree_is_in_range(&image_tree, (uintptr_t)obj) == in_image' failed. [908] signal 6 (-6): Aborted in expression starting at none:0 unknown function (ip: 0x79ea4cef9ebc) at /lib/x86_64-linux-gnu/libc.so.6 gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x79ea4ce95394) at /lib/x86_64-linux-gnu/libc.so.6 __assert_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) jl_object_in_image at /source/src/staticdata.c:216:5 [inlined] jl_object_in_image at /source/src/staticdata.c:210:22 needs_uniquing at /source/src/staticdata.c:422:5 jl_insert_into_serialization_queue at /source/src/staticdata.c:606:45 jl_insert_into_serialization_queue at /source/src/staticdata.c:867:17 jl_serialize_reachable at /source/src/staticdata.c:1050:13 jl_save_system_image_to_stream at /source/src/staticdata.c:3098:9 [inlined] ijl_create_system_image at /source/src/staticdata.c:3473:5 ijl_write_compiler_output at /source/src/precompile.c:140:5 ijl_atexit_hook at /source/src/init.c:276:9 jl_repl_entrypoint at /source/src/jlapi.c:1157:9 main at /source/cli/loader_exe.c:117:15 unknown function (ip: 0x79ea4ce96249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S Allocations: 6251118 (Pool: 6250879; Big: 239); GC: 11 ✗ SnpArrays ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("4e780e97-f5bf-4111-9dc4-b70aaf691b06"), "SnpArrays") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] __require_prelocked(pkg::Base.PkgId, env::String) @ Base loading.jl:2891 [3] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base loading.jl:2739 [4] macro expansion @ loading.jl:2653 [inlined] [5] macro expansion @ lock.jl:376 [inlined] [6] __require(into::Module, mod::Symbol) @ Base loading.jl:2617 [7] require(into::Module, mod::Symbol) @ Base loading.jl:2593 [inlined] [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) @ Base module.jl:36 [inlined] [9] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base module.jl:60 [10] _eval_using(to::Module, path::Expr, flags::UInt8) @ Base module.jl:137 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:14 [12] include(mod::Module, _path::String) @ Base Base.jl:329 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base loading.jl:3359 [14] top-level scope @ stdin:5 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:3 in expression starting at stdin:5 ✗ MendelIHT 134 dependencies successfully precompiled in 543 seconds. 40 already precompiled. 3 dependencies had output during precompilation: ┌ SnpArrays │ julia: /source/src/staticdata.c:216: jl_object_in_image: Assertion `eyt_tree_is_in_range(&image_tree, (uintptr_t)obj) == in_image' failed. │ │ [908] signal 6 (-6): Aborted │ in expression starting at none:0 │ unknown function (ip: 0x79ea4cef9ebc) at /lib/x86_64-linux-gnu/libc.so.6 │ gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ unknown function (ip: 0x79ea4ce95394) at /lib/x86_64-linux-gnu/libc.so.6 │ __assert_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ jl_object_in_image at /source/src/staticdata.c:216:5 [inlined] │ jl_object_in_image at /source/src/staticdata.c:210:22 │ needs_uniquing at /source/src/staticdata.c:422:5 │ jl_insert_into_serialization_queue at /source/src/staticdata.c:606:45 │ jl_insert_into_serialization_queue at /source/src/staticdata.c:867:17 │ jl_serialize_reachable at /source/src/staticdata.c:1050:13 │ jl_save_system_image_to_stream at /source/src/staticdata.c:3098:9 [inlined] │ ijl_create_system_image at /source/src/staticdata.c:3473:5 │ ijl_write_compiler_output at /source/src/precompile.c:140:5 │ ijl_atexit_hook at /source/src/init.c:276:9 │ jl_repl_entrypoint at /source/src/jlapi.c:1157:9 │ main at /source/cli/loader_exe.c:117:15 │ unknown function (ip: 0x79ea4ce96249) at /lib/x86_64-linux-gnu/libc.so.6 │ __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S │ Allocations: 6251118 (Pool: 6250879; Big: 239); GC: 11 └ ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ ┌ MendelIHT │ ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("4e780e97-f5bf-4111-9dc4-b70aaf691b06"), "SnpArrays") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) │ Stacktrace: │ [1] error(s::String) │ @ Base error.jl:56 │ [2] __require_prelocked(pkg::Base.PkgId, env::String) │ @ Base loading.jl:2891 │ [3] _require_prelocked(uuidkey::Base.PkgId, env::String) │ @ Base loading.jl:2739 │ [4] macro expansion │ @ loading.jl:2653 [inlined] │ [5] macro expansion │ @ lock.jl:376 [inlined] │ [6] __require(into::Module, mod::Symbol) │ @ Base loading.jl:2617 │ [7] require(into::Module, mod::Symbol) │ @ Base loading.jl:2593 [inlined] │ [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) │ @ Base module.jl:36 [inlined] │ [9] eval_import_path_all(at::Module, path::Expr, keyword::String) │ @ Base module.jl:60 │ [10] _eval_using(to::Module, path::Expr, flags::UInt8) │ @ Base module.jl:137 [inlined] │ [11] top-level scope │ @ ~/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:14 │ [12] include(mod::Module, _path::String) │ @ Base Base.jl:329 │ [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) │ @ Base loading.jl:3359 │ [14] top-level scope │ @ stdin:5 │ in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:3 │ in expression starting at stdin:5 └ ERROR: LoadError: The following 2 packages failed to precompile: SnpArrays Failed to precompile SnpArrays [4e780e97-f5bf-4111-9dc4-b70aaf691b06] to "/home/pkgeval/.julia/compiled/v1.14/SnpArrays/jl_0gAGhV" (ProcessSignaled(6)). MendelIHT Failed to precompile MendelIHT [921c7187-1484-5754-b919-5d3ed9ac03c4] to "/home/pkgeval/.julia/compiled/v1.14/MendelIHT/jl_Hfj9um" (ProcessExited(1)). in expression starting at /PkgEval.jl/scripts/precompile.jl:34 Precompilation failed after 560.68s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_zbnHQS/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.130 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.14.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_zbnHQS/Manifest.toml` [7d9f7c33] Accessors v0.1.45 [79e6a3ab] Adapt v4.7.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.28.1 [67c07d97] Automa v1.2.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.8.0 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.16 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.12 [f70d9fcc] CommonWorldInvalidations v1.1.1 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.2.0 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.130 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.17.0 [38e38edf] GLM v1.9.5 [a0844989] Gamma v1.1.0 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.29 [09f84164] HypothesisTests v0.11.8 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v1.0.1 [bdcacae8] LoopVectorization v0.12.174 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v2.0.1 [90014a1f] PDMats v0.11.40 [69de0a69] Parsers v2.8.6 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.6 [fdea26ae] SIMD v3.7.2 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.46 [0aa819cd] SQLite v1.8.1 [431bcebd] SciMLPublic v1.2.4 [91c51154] SentinelArrays v1.4.10 [1277b4bf] ShiftedArrays v2.0.0 [4e780e97] SnpArrays v0.3.23 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.8.0 [aedffcd0] Static v1.4.4 [0d7ed370] StaticArrayInterface v1.10.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [3eaba693] StatsModels v0.7.10 [892a3eda] StringManipulation v0.4.6 [ec057cc2] StructUtils v2.8.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.13.0 [8290d209] ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.74 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [76ed43ae] SQLite_jll v3.53.2+0 [ffd25f8a] XZ_jll v5.8.3+0 [c4b69c83] dlfcn_win32_jll v1.4.2+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] LibCURL_jll v8.21.0+0 [e37daf67] LibGit2_jll v1.9.6+0 [29816b5a] LibSSH2_jll v1.11.103+0 [14a3606d] MozillaCACerts_jll v2026.7.16 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.7+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... julia: /source/src/staticdata.c:216: jl_object_in_image: Assertion `eyt_tree_is_in_range(&image_tree, (uintptr_t)obj) == in_image' failed. [922] signal 6 (-6): Aborted in expression starting at none:0 unknown function (ip: 0x7082f7b68ebc) at /lib/x86_64-linux-gnu/libc.so.6 gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x7082f7b04394) at /lib/x86_64-linux-gnu/libc.so.6 __assert_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) jl_object_in_image at /source/src/staticdata.c:216:5 [inlined] jl_object_in_image at /source/src/staticdata.c:210:22 needs_uniquing at /source/src/staticdata.c:422:5 jl_insert_into_serialization_queue at /source/src/staticdata.c:606:45 jl_insert_into_serialization_queue at /source/src/staticdata.c:867:17 jl_serialize_reachable at /source/src/staticdata.c:1050:13 jl_save_system_image_to_stream at /source/src/staticdata.c:3098:9 [inlined] ijl_create_system_image at /source/src/staticdata.c:3473:5 ijl_write_compiler_output at /source/src/precompile.c:140:5 ijl_atexit_hook at /source/src/init.c:276:9 jl_repl_entrypoint at /source/src/jlapi.c:1157:9 main at /source/cli/loader_exe.c:117:15 unknown function (ip: 0x7082f7b05249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S Allocations: 6250805 (Pool: 6250566; Big: 239); GC: 11 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("4e780e97-f5bf-4111-9dc4-b70aaf691b06"), "SnpArrays") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] __require_prelocked(pkg::Base.PkgId, env::String) @ Base loading.jl:2891 [3] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base loading.jl:2739 [4] macro expansion @ loading.jl:2653 [inlined] [5] macro expansion @ lock.jl:376 [inlined] [6] __require(into::Module, mod::Symbol) @ Base loading.jl:2617 [7] require(into::Module, mod::Symbol) @ Base loading.jl:2593 [inlined] [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) @ Base module.jl:36 [inlined] [9] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base module.jl:60 [10] _eval_using(to::Module, path::Expr, flags::UInt8) @ Base module.jl:137 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:14 [12] include(mod::Module, _path::String) @ Base Base.jl:329 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base loading.jl:3359 [14] top-level scope @ stdin:5 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:3 in expression starting at stdin:5 2 dependencies had output during precompilation: ┌ SnpArrays │ julia: /source/src/staticdata.c:216: jl_object_in_image: Assertion `eyt_tree_is_in_range(&image_tree, (uintptr_t)obj) == in_image' failed. │ │ [922] signal 6 (-6): Aborted │ in expression starting at none:0 │ unknown function (ip: 0x7082f7b68ebc) at /lib/x86_64-linux-gnu/libc.so.6 │ gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ unknown function (ip: 0x7082f7b04394) at /lib/x86_64-linux-gnu/libc.so.6 │ __assert_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ jl_object_in_image at /source/src/staticdata.c:216:5 [inlined] │ jl_object_in_image at /source/src/staticdata.c:210:22 │ needs_uniquing at /source/src/staticdata.c:422:5 │ jl_insert_into_serialization_queue at /source/src/staticdata.c:606:45 │ jl_insert_into_serialization_queue at /source/src/staticdata.c:867:17 │ jl_serialize_reachable at /source/src/staticdata.c:1050:13 │ jl_save_system_image_to_stream at /source/src/staticdata.c:3098:9 [inlined] │ ijl_create_system_image at /source/src/staticdata.c:3473:5 │ ijl_write_compiler_output at /source/src/precompile.c:140:5 │ ijl_atexit_hook at /source/src/init.c:276:9 │ jl_repl_entrypoint at /source/src/jlapi.c:1157:9 │ main at /source/cli/loader_exe.c:117:15 │ unknown function (ip: 0x7082f7b05249) at /lib/x86_64-linux-gnu/libc.so.6 │ __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) │ unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S │ Allocations: 6250805 (Pool: 6250566; Big: 239); GC: 11 └ ┌ MendelIHT │ [Output was shown above] └ ERROR: LoadError: The following 2 packages failed to precompile: SnpArrays Failed to precompile SnpArrays [4e780e97-f5bf-4111-9dc4-b70aaf691b06] to "/home/pkgeval/.julia/compiled/v1.14/SnpArrays/jl_BImhgN" (ProcessSignaled(6)). MendelIHT Failed to precompile MendelIHT [921c7187-1484-5754-b919-5d3ed9ac03c4] to "/home/pkgeval/.julia/compiled/v1.14/MendelIHT/jl_jhqgv1" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:1 Testing failed after 54.68s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 698.14s: package fails to precompile